1H NMR spectroscopy of aqueous faecal extracts has been used to investigate differences in metabolic activity of gut microbiota in patients with ulcerative colitis (UC) (n = 13), irritable bowel syndrome (IBS) (n = 10) and healthy controls (C) (n = 22). Up to four samples per individual were collected over two years giving a total of 124 samples. Multivariate discriminant analysis, based on NMR data from all three groups, was able to predict UC and C group membership with good sensitivity and specificity; classification of IBS samples was less successful and could not be used for diagnosis. Trends were detected toward increased taurine and cadaverine levels in UC with increased bile acid and decreased branched chain fatty acids in IBS relative to controls; changes in short chain fatty acids and amino acids were not significant. Previous PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis of the same faecal material had shown alterations of the gut microbiota when comparing UC and IBS groups with controls. Hierarchical Cluster Analysis showed that DGGE profiles from the same individual were stable over time but NMR spectra were more variable; Canonical Correlation Analysis of NMR and DGGE data partly separated the three groups and revealed a correlation between the gut microbiota profile and metabolite composition.